Jenkins can't generate HTML reports with htmlpublisher
What version of Jenkins are you running? I'm seeing this issue on all of my projects since updating to 1.529. The files are being copied to jobs/ correctly as you mentioned.
The answer you accepted is incorrect and contradicts the documentation at https://wiki.jenkins-ci.org/display/JENKINS/HTML+Publisher+Plugin
EDIT: The issue has been resolved in 1.530: https://jenkins-ci.org/changelogI've updated and I'm not seeing 404s anymore.
The developers of Jenkins has confirmed that this issue is related to the version 1.529 and it is solved in 1.530.